At 8:00 p.m. on October 8, 2009, Univision's WCAA moved to the 96.3 FM frequency while WQXR-FM moved to 105.9 FM becoming a non-commercial radio station run by WNYC.[1][2] Within that next week WCAA, now on 96.3, changed its call letters to WXNY-FM.

The station broadcasts mainly classical music recordings. One of the station's listeners was the inventor of frequency modulation, Edwin Howard Armstrong. When Armstrong put his experimental FM station, W2XMN, on the air, he arranged to rebroadcast some of WQXR's programming. This ended in 1939, when Hogan and Sanger put their own experimental FM station on the air, W2XQR, just down the dial from Armstrong at 42.3 MHz.

When the Federal Communications Commission began licensing commercial FM stations, W2XQR moved to 45.9 MHz and became W59NY; the special FM callsigns were later dropped and the station became WQXQ.

In 1944, Hogan and Sanger sold their holding company, Interstate Broadcasting Company, to the New York Times Company. When the FM band was moved from 42–50 MHz to its present frequency range of 88–108 MHz in 1945, WQXQ moved to 97.7 MHz. Within a few years, the station had adopted its current callsign, WQXR-FM, and its frequency for the next 64 years, 96.3 MHz.

Older logo of WQXR displaying both FM and AM frequencies

WQXR was the first AM station in New York to experiment with broadcasting in stereo, beginning in 1952. During some of its live concerts, it used two microphones positioned six feet apart. The microphone on the right led to its AM feed, and the one on the left to its FM feed, so a listener could position two radios six feet apart, one tuned to 1560 and the other to 96.3, and listen in stereo.

During the 1950s, WQXR-FM's programming was also heard on the Rural Radio Network in Upstate New York; this ended when the RRN stations were sold to Pat Robertson's new Christian Broadcasting Network. Both the AM and FM sides continued to simulcast each other until 1965, when the FCC began requiring commonly owned AM and FM stations in large markets to broadcast separate programming for at least part of the day.

After briefly attempting to sell the WQXR stations in 1971, The New York Times was able to get a waiver of the simulcasting rules. The stations continued to duplicate each other until 1992, when the AM side changed its programming from classical to popular standards, becoming WQEW. In 1998, the Times entered into a long-term lease for WQEW with ABC, a move which brought Radio Disney to New York City. The Times Company also included a purchase clause in the lease contract, and ABC exercised the option in 2007. This left WQXR-FM as the Times 's lone radio station and, following a sale of its group of television stations to Local TV that same year, the Times Company's sole remaining broadcasting property.

On July 14, 2009, the New York Times Company announced it was trading the 96.3 frequency to Univision Radio in return for the 105.9 frequency of Univision's WCAA. The sale was slated to close in the second half of 2009. At 8 p.m. on October 8, 2009, WCAA and WQXR traded frequencies.

The frequency swap was part of a three-way deal between Univision, the New York Times Company and WNYC. Univision paid the New York Times Company $33.5 million to trade broadcasting licenses with the Times. WNYC then paid the New York Times Company $11.5 million for 105.9 FM’s license, equipment and the WQXR call letters and website (changing the web domain from wqxr.com to wqxr.org) [2] As a result of the deal, WQXR became a non-commercial public radio station operated by WNYC, and now runs three on-air pledge drives a year.

WQXR has less range and population coverage on 105.9 than it had with its old signal on 96.3. WQXR's old and new signals both radiate from the same FM master antenna atop the Empire State Building; but while WQXR's old signal (now WCAA's) is 6,000 watts ERP (effective radiated power—the energy concentrated toward the horizon), its new signal (WCAA's old one) is 600 watts. The calculated signal strength of the new signal at 30 miles (covering about 14.5 million people) is the same as the old 96.3 FM signal at 42 miles (covering about 17.1 million people). Further compromising coverage is Hartford's WHCN, which also broadcasts on 105.9 FM. While WHCN has a directional signal with reduced wattage toward WQXR's transmitter, the two stations do interfere with each other where their signals overlap.

Worldwide, WQXR's standard programming is available on its Webcast, and the station also has a Webcast called Q2, focusing on classical works by living composers. Q2's daily playlist is called Living Music, Living Composers.[7]

As with most remaining classical music stations in the U.S., the station's playlist has changed over the years to focus on shorter and more easily assimilated pieces and away from long pieces and most vocal music including opera. However, when compared to music programming from WQXR's early days (1940s and 1950s) the change in music is not as pronounced as might be expected. The station does, however, play a fair amount of 20th-century classical works. It also continues to play long pieces during special broadcasts, and during evening hours (7 p.m. to 6 a.m.) and also broadcasts a complete opera at least once a week. Most notably, it is the headquarters for broadcasting the Metropolitan Opera radio broadcasts each Saturday afternoon during its season, from December to April.

In addition to music, WQXR had newscast and financial updates of various lengths, from thirty seconds to three minutes, prepared initially by Bloomberg Radio (WBBR-AM 1130 kHz New York City). Over the years, the prominence that WQXR afforded to news first rose, then steadily diminished. During the 1950s and 1960s, WQXR provided five minutes of news each hour, uninterrupted by commercials. "Every hour on the hour, the New York Times brings you the latest news bulletins." These bulletins focused heavily on New York City, New York State, national, and international developments. It also featured a weather forecast for the New York Metropolitan area. Sports was almost never included. This presentation expanded during the 1960s to a fifteen-minute "early evening news roundup" at 6:00 p.m. WQXR dissolved its two-person news department in late 2008. It had broadcast from the actual newsroom of The New York Times at 229 West 43rd Street, 1.4 miles from WQXR's studios at Fifth Avenue and 18th Street.

WQXR relied on New York Times contributors for a number of short-form features, such as "The Front Page of Tomorrow's New York Times" broadcast six evenings at 9:00 PM and prepared by Times reporter James Barron, also a weekly fifteen-minute book feature prepared in conjunction with the New York Times Book Review editors, a weekly review of dance, and weekday reports on theatre, dining and wine. The New York Times White House correspondent also had frequent reports which were aired during the Morning Show. Since the transfer of ownership to WNYC, the station has aired brief news updates during drive time from the WNYC newsroom.

The station also features a weekly program about piano entitled Reflections from the Keyboard, which is hosted by David Dubal. Dubal had previously been music director at WNCN (a defunct classical-music radio station in New York City), WQXR's competitor in the 1960s, 1970s, and 1980s. No new episodes of the program were aired from August 2009-June 2013. Reflections from the Keyboard returned to WQXR in June 2013 after a four year hiatus. Before it returned, Dubal hosted a program than ran for two months called The Romantic Piano from April to June 2013. Many of the current WQXR announcers, as well as its program director, were previously employed at WNCN. WQXR's national programs include New York Philharmonic This Week hosted by Alec Baldwin, Exploring Music hosted by Bill McGlaughlin, Performance Today hosted by Fred Child, Pipedreams hosted by Michael Barone and From The Top hosted by Christopher O'Riley. David Garland hosts two shows on WQXR each week: Movies on the Radio, a show that has a different movie theme each week, and airs on Saturdays at 9PM; he also hosts Old School, a program that plays old time classical pieces. Bob Sherman hosts The McGraw Hill Financial Young Artist's Showcase, which displays the talents of young emerging artists. The show airs Wednesday Nights at 9PM (The show, during WQXR's ownership by The New York Times, aired at 9:05 PM because of James Barron's Front Page of The New York Times.) The showcase has been airing on WQXR since 1978.